Is there any method to make almost an automatic 'hive'?
I'd start with 6-sided cylinders, and array modifiers:


1st modifier to create a duplicate at a diagonal offset (x:0.5, y:0.766 ) 
2nd modifier for 1 row in say the x-direction (x:.667, and not 1, as the boundig box covers both the cylinders)
3rd modifier to fill the plane in the y direction (y:0.857)


Then I'd either apply the modifiers and remove unwanted geometry, or use boolean modifiers to create holes where I want them (or to limit the structure to a given volume).

The black grooves can be a simple plane, or you can slighty modify the initial cylinder (and/or adapt the array offsets if needed) by extruding the lower set of edges outward. Close the other end of the basic cylinder for the yellow plates.